def test__to_dict_2(self):
contact = Contact(1, 2, 1.0)
contact.true_positive = True
contact.lower_bound = 4
answer_dict = {
"id": (1, 2),
"true_positive": True,
"false_positive": False,
"status_unknown": False,
"distance_bound": (4.0, 8.0),
"lower_bound": 4.0,
"upper_bound": 8.0,
"raw_score": 1.0,
"res1": "X",
"res2": "X",
"res1_chain": "",
"res2_chain": "",
"res1_seq": 1,
"res2_seq": 2,
"res1_altseq": 0,
"res2_altseq": 0,
"scalar_score": 0.0,
"status": 1,
"weight": 1.0,
}
contact_dict = contact._to_dict()
for k in answer_dict.keys():
self.assertEqual(answer_dict[k], contact_dict[k],
"Key {} differs".format(k))
def test__to_dict_2(self):
contact = Contact(1, 2, 1.0)
contact.true_positive = True
contact.lower_bound = 4
answer_dict = {
'id': (1, 2),
'true_positive': True,
'false_positive': False,
'status_unknown': False,
'distance_bound': (4.0, 8.0),
'lower_bound': 4.0,
'upper_bound': 8.0,
'raw_score': 1.0,
'res1': 'X',
'res2': 'X',
'res1_chain': '',
'res2_chain': '',
'res1_seq': 1,
'res2_seq': 2,
'res1_altseq': 0,
'res2_altseq': 0,
'scalar_score': 0.0,
'status': 1,
'weight': 1.0,
}
contact_dict = contact._to_dict()
for k in answer_dict.keys():
self.assertEqual(answer_dict[k], contact_dict[k],
"Key %s differs" % k)
def test_true_positive_1(self):
contact = Contact(1, 2, 1.0)
self.assertFalse(contact.true_positive)
contact.true_positive = True
self.assertTrue(contact.true_positive)
def test_status_1(self):
contact = Contact(1, 2000000, 1.0)
self.assertEqual(ContactMatchState.unknown.value, contact.status)
contact.true_positive = True
self.assertEqual(ContactMatchState.true_positive.value, contact.status)
def _read(self, structure, f_id, distance_cutoff, atom_type):
"""Read a contact file
Parameters
----------
structure
A :obj:`~Bio.PDB.Structure.Structure>` instance
f_id : str
Unique contact file identifier
distance_cutoff : int
Distance cutoff for which to determine contacts
atom_type : str
Atom type between which distances are calculated
Returns
-------
:obj:`~conkit.core.contactfile.ContactFile~`
"""
hierarchies = []
for model in structure:
hierarchy = ContactFile(f_id + '_' + str(model.id))
chains = list(chain for chain in model)
for chain in chains:
self._remove_hetatm(chain)
self._remove_atom(chain, atom_type)
for chain1, chain2 in itertools.product(chains, chains):
if chain1.id == chain2.id: # intra
contact_map = ContactMap(chain1.id)
else: # inter
contact_map = ContactMap(chain1.id + chain2.id)
for (atom1, atom2,
distance) in self._chain_contacts(chain1, chain2):
contact = Contact(atom1.resseq,
atom2.resseq,
round(1.0 - (distance / 100), 6),
distance_bound=(0.,
float(distance_cutoff)))
contact.res1_altseq = atom1.resseq_alt
contact.res2_altseq = atom2.resseq_alt
contact.res1 = atom1.resname
contact.res2 = atom2.resname
contact.res1_chain = atom1.reschain
contact.res2_chain = atom2.reschain
if distance_cutoff == 0 or distance < distance_cutoff:
contact.true_positive = True
contact_map.add(contact)
if contact_map.empty:
del contact_map
else:
if len(contact_map.id) == 1:
contact_map.sequence = self._build_sequence(chain1)
assert len(contact_map.sequence.seq) == len(chain1)
else:
contact_map.sequence = self._build_sequence(chain1) \
+ self._build_sequence(chain2)
assert len(contact_map.sequence.seq) \
== len(chain1) + len(chain2)
hierarchy.add(contact_map)
hierarchy.method = 'Contact map extracted from PDB ' + str(
model.id)
hierarchy.remark = [
'The model id is the chain identifier, i.e XY equates to chain X and chain Y.',
'Residue numbers in column 1 are chain X, and numbers in column 2 are chain Y.'
]
hierarchies.append(hierarchy)
if len(hierarchies) > 1:
msg = "Super-level to contact file not yet implemented. " \
"Parser returns hierarchy for top model only!"
warnings.warn(msg, FutureWarning)
return hierarchies[0]
